internal static IWittyerBnd Create([NotNull] IVcfVariant variant,
IVcfVariant secondVariant, [CanBeNull] string sampleName,
double percentageDistance, uint basepairDistance, IReadOnlyList <uint> bins)
{
var(first, second) = MiscUtils.FindBndEntriesOrder(variant, secondVariant);
var posInterval = first.CalculateBndBorderInterval(second,
first.ParseCi(WittyerConstants.Cipos), percentageDistance, basepairDistance);
var endInterval = second.CalculateBndBorderInterval(first,
second.ParseCi(WittyerConstants.Cipos), percentageDistance,
basepairDistance);
var svType = variant.ParseWittyerVariantType(sampleName);
var winner = GetWinner();
var overlapInfo = new List <OverlapAnnotation>();
var sample = WittyerSample.CreateOverall(variant, sampleName, false);
return(Create(first, posInterval, winner, endInterval, overlapInfo, sample, second, svType));
Winner GetWinner()
{
if (svType == WittyerVariantType.TranslocationBreakend)
{
return(Winner.Create(svType));
}
if (svType != WittyerVariantType.Insertion)
{
return(Winner.Create(svType, BedInterval.Create(first.Position, second.Position + 1), bins));
}
uint?end = null;
// insertion, try sequences first
if (variant.IsSimpleSequence(out var length))
{
end = length;
}
// try svlength, but if not, assume unknown length.
else if (variant.TryGetSvLength(out length) == null)
{
end = length;
}
return(Winner.Create(svType, end == null ? null : BedInterval.Create(variant.Position, variant.Position + end.Value), bins));
}
}
